But The Daily Telegraph newspaper said Thursday more senior public servants in the department were receiving much higher performance payments, and the total could top the 53 million pounds handed out last financial year.
The Daily Mail newspaper said the figures showed 287 million pounds had been paid in bonuses since the war in Iraq started in 2003.
The figures come as public criticism of Britain's involvement in the Afghan conflict against Taliban insurgents grows amid rising numbers of troop deaths.
Prime Minister Gordon Brown has been under intense pressure over Britain's strategy, as military experts and families accuse the government of failing to properly support and equip troops on the frontline.
The figures were released in parliament on Wednesday by junior defence minister Kevan Jones in a written response to questions from the main opposition Conservatives.
"These pay awards are met from within salary budget and have no impact on the operational or equipment budget," a ministry spokesman said.
"Pay awards were given to around 50,000 civil servants resulting in an average payment of less than 1,000 pounds."
Lee Mackie, whose son Jason, 21, was killed in Afghanistan in May, said the money would have been better spent helping serving soldiers.
"Every foot soldier is basically earning nothing. But they can give these huge bonuses while our boys give up their lives," the mother of three said.
"They all sit their behind their desks, not risking their lives, and yet they're earning these huge amounts of money."
Britain has lost 95 soldiers in Afghanistan this year, the highest casualty levels since the 1982 Falklands War, and a total of 232 have died since the 2001 invasion of the country.
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